Malnutrition among hospitalized children is often misdiagnosed and untreated. This study aimed to compare STRONGkids and PYMS screening tools for determining the risk of malnutrition in hospitalized children. This cross-sectional study was conducted among patients aged 2-to-18 years in tertiary-care hospitals in Indonesia. Demographic data, illnesses, and nutritional assessment based on STRONGkids and PYMS methods were measured within 24-48 hours of admission. The sensitivity, specificity, and positive and negative predictive values of STRONGkids and PYMS for detecting hospital malnutrition were evaluated, with the percentage of weight loss between admission and discharge standing as the gold standard. Out of 48 patients, 54.2% were male with a median age of 11 years. Hematological disease comprised 52.1% of the study’s participants with hospital stays ranging from 3 to 22 days. The prevalence of hospital malnutrition was 25%. The accuracy level of STRONGkids was 70.8% in detecting hospital malnutrition, whereas PYMS was 52%. The sensitivity, specificity, and positive and negative predictive values (PPV and NPV) of STRONGkids for detecting hospital malnutrition were 41.7%, 80.6%, 41.7%, and 80.6%, respectively, whereas PYMS had 83.3% sensitivity, 41.7% specificity, 32.3% PPV, and 88.2% NPV. STRONGkids performed better than PYMS in predicting the probability of hospital malnutrition. Our findings support the use of STRONGkids as a nutritional risk screening tool in hospitalized children in Indonesia.